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-lactamase and housekeeping gene sequences as well as ERIC-1R PCR typing
1 Service de Microbiologie-Hygiène, Hôpital Ambroise Paré AP-HP, Université Versailles-Saint-Quentin-en-Yvelines-UFR Médicale Paris-Ile-de-France-Ouest, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France
2 Laboratoire de Microbiologie Médicale, Fondation Hôpital Saint-Joseph, Paris, France
3 Centre de Biologie et d'Ecologie Tropicale et Méditerranéenne, UMR 5555, Université de Perpignan, France
4 Service de Microbiologie, Centre Hospitalier du Pays d'Aix, Aix en Provence, France
Correspondence
Marie-Hélène Nicolas-Chanoine
marie-helene.nicolas-chanoine{at}apr.ap-hop-paris.fr
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ABSTRACT |
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-lactamase-producing K. oxytoca isolates displayed two distinguishable enterobacterial repetitive intergenic consensus (ERIC)-1R profiles. It was hypothesized that the two groups of chromosomal -lactamases might correspond to two groups of strains in the K. oxytoca taxon. To confirm this hypothesis, clinical isolates and reference strains of K. oxytoca were studied by determination of the sequence of their blaOXY genes, and of a partial fragment of their 16S rRNA (387 bp) and rpoB (512 bp) genes. The sequence data were phylogenetically analysed by using the parsimony method. Four clinical isolates possessed a blaOXY-1 gene and nine possessed a blaOXY-2 gene. The mean percentage of rpoB and 16S rRNA gene identity was >99 % within each group of strains, whereas it was 96·56±0·24 % for rpoB genes and 97·80±0·22 % for 16S rRNA genes between the group of strains harbouring the blaOXY-1 gene and the group harbouring the blaOXY-2 gene. The phylogenetic tree resulting from combined analysis of the 16S rRNA and rpoB datasets showed that the K. oxytoca isolates were monophyletic and separated into two clades; these clades included strains with either the blaOXY-1 gene or the blaOXY-2 gene. This result was supported with high bootstrap values of 97 and 99 %, respectively. Moreover, the two groups of strains displayed distinct ERIC-1R profiles, with bands characteristic of each profile. Thus, the chromosomal blaOXY gene sequence is able to delineate not only two groups of -lactamases in K. oxytoca, but also two clades in the K. oxytoca taxon, in a manner similar to the sequence of housekeeping genes. These results suggest that K. oxytoca should be divided into two genetic groups, group OXY-1 represented by K. oxytoca strain SL781 (=CIP 104963) and group OXY-2 by K. oxytoca strain SL911 (=CIP 106098).
Published online ahead of print on 23 August 2002 as DOI 10.1099/ijs.0.02408-0.
Alignments of consensus DNA sequences of the 16S rRNA and and rpoB genes are available as supplementary data in IJSEM Online.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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; Jeong et al., 2001; Reiss et al., 2000) and also in antibiotic-associated diarrhoea (Benoit et al., 1992; Högenauer et al., 1998; Terrier et al., 1995).
Methods routinely used for species identification are not able to differentiate K. oxytoca from the other indole-positive Klebsiella species: Klebsiella ornithinolytica, Klebsiella planticola and Klebsiella terrigena (Monnet et al., 1991). However, recent molecular studies have definitively demonstrated that K. oxytoca is phylogenetically distant from the other indole-positive Klebsiella species, on the basis of 16S rRNA and rpoB gene sequence analysis (Drancourt et al., 2001). For this reason, the indole-positive Klebsiella species other than K. oxytoca have recently been renamed as Raoultella species (Drancourt et al., 2001).
Both K. oxytoca and Raoultella species are naturally resistant to amino- and carboxypenicillins, but are susceptible to the amoxicillin–clavulanate combination (Stock & Wiedemann, 2001). Until now, the chromosomal -lactamase responsible for this -lactam-resistance phenotype has been defined only for K. oxytoca, and was shown to belong to class A of the -lactamases. Although its production is not regulated, up-mutations induce its overproduction, resulting in the resistance of isolates to certain third-generation cephalosporins (ceftriaxone and cefotaxime) and aztreonam (Fournier et al., 1994).
Fournier et al. (1996b) have determined two groups of chromosomal -lactamase in K. oxytoca, OXY-1 and OXY-2, with isoelectric points ranging from 7·1 to 8·8 and 5·2 to 6·8, respectively. The corresponding genes, blaOXY-1 and blaOXY-2, display a nucleotide sequence identity of 87 %. Whilst searching for a molecular method to identify the different species of Raoultella and K. oxytoca, we observed that the OXY-1 -lactamase-producing and the OXY-2 -lactamase-producing isolates displayed two distinct profiles generated by the enterobacterial repetitive intergenic consensus (ERIC)-1R PCR typing system, and that each profile had characteristic bands. Faced with such a result, we hypothesized that the two groups of -lactamases (OXY-1 and OXY-2) of K. oxytoca might correspond to two groups of strains in the K. oxytoca taxon. We confirmed this hypothesis by studying the sequence of the blaOXY, 16S rRNA and rpoB genes in epidemiologically non-related clinical isolates of K. oxytoca and reference strains.
To our knowledge, this study is the first to show that chromosomal -lactamase genes are able to identify clades within a given species, as do housekeeping genes such as 16S rDNA and rpoB.
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METHODS |
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-lactamases, respectively. Those clinical isolates (n=10: SG12, SG49, SG337, SG344, SG43, SG69, SG77, SG9, SG4 and SG62) that displayed an extended spectrum of resistance to certain -lactam molecules (ceftriaxone, cefotaxime and aztreonam) had been collected between 1984 and 1998, in six French hospitals representing the northern and southern regions of France and the Paris area. The three remaining isolates (SG74, SG81 and SG176) were susceptible to third-generation cephalosporins and aztreonam, and were obtained from three patients hospitalized in the Saint Joseph hospital in 1999 and 2000.
Mating-out assays and plasmid content analysis.
Transfer of -lactam resistance to Escherichia coli K-12C600S1000 (StrR) was attempted by liquid and solid mating-out assays. The recipient and donor cells were mixed in a ratio of 1 : 1 and incubated in broth with moderate shaking at 37 °C for 1 h. Five hundred microlitres of each mixture was plated out on tryptic soy agar (TSA) plates and incubated overnight at 37 °C. Transconjugants were selected on Drigalski agar containing ampicillin (20 mg l-1) and streptomycin (100 mg l-1). Clinical isolates of K. oxytoca were examined for their plasmid DNA content by the procedure of Birnboim (1983).
DNA preparation.
DNA templates were prepared by suspending a freshly grown colony in 500 µl lysis buffer (20 mM Tris/HCl pH 8·3, 50 mM KCl, 0·1 % Tween 20) and heating at 94 °C for 10 min. DNA preparations were stored at -20 °C.
Gene amplification and sequencing.
To amplify the promoter and the coding regions of the blaOXY genes, two primers were designed, one upstream from the promoter region (OXY-A: 5'-TCGGTAACTGTGACGGGA-3') and one downstream from the coding region (OXY-B: 5'-CCGAATTTCGGGAAGCCA-3'), on the basis of the blaOXY sequences published previously. These primers generate a fragment of 1040 bp. The PCR mixture contained 20 mM Tris/HCl pH 8·0, 100 mM KCl, 1·5 mM MgCl2, 500 µM each dNTP, 0·2 µM each primer and 0·0025 U Taq DNA polymerase µl-1. The amplification reaction consisted of a pre-PCR stage (at 94 °C for 5 min, at 51 °C for 1 min and at 72 °C for 1 min), and then 45 cycles at 94 °C for 30 s, at 51 °C for 30 s and at 72 °C for 30 s, and a final extension step at 72 °C for 10 min.
16S rDNA was amplified with two primers complementary to highly conserved regions in Gram-negative rRNA (A12, 5'-AAGCCTGATGCAGCCA-3'; A13, 5'-TTTCGCACCTGAGCGT-3'). The amplified fragment, which displays a great nucleotide variability in Gram-negative bacteria, starts at position 381 and ends at position 767 (387 bp) relative to the E. coli 16S rDNA sequence. The PCR mixture was identical to that described above, except for the MgCl2 concentration, which was higher (2·5 mM). The reaction was performed with a pre-denaturation step for 5 min at 95 °C, then 35 cycles for 1 min at 95 °C, for 1 min at 45 °C and for 1 min at 72 °C, followed by a final extension step at 72 °C for 10 min.
The rpoB gene was partially amplified (512 bp) by using the primers CM32B and CM81B, together with the conditions described by Mollet et al. (1997). The first nucleotide of the fragment studied corresponds to codon 500 of the 1342 aa coding region in E. coli.
PCR products were sequenced by using an automated cycle sequencing system, with the same primers as for the PCR. However, for the blaOXY gene, two additional internal primers were selected, OXY-C (5'-TATTAAAACAGAG-3') and OXY-D (5'-ATTAGAGGTCGGAA-3'), to obtain two additional priming sites for sequencing.
Sequence data analysis.
Single sequence alignments were performed by using BLAST 2 sequence software (Tatusova & Madden, 1999), whereas multiple sequence alignments were performed with DIALIGN 2 software (Morgenstern, 1999). The blaOXY gene sequences of our isolates were compared with those of reference strains SL781 (blaOXY-1) and SL911 (blaOXY-2) whose GenBank acession numbers are Z30177 and Z49084, respectively. The rpoB and 16S rDNA consensus sequences were constructed by using CAP software (Huang, 1992).
Tree reconstruction.
Phylogenetic analyses were based on parsimony and were performed using version 4.0b5 of PAUP* (Swofford, 1998). Separate analysis was performed for each of the rpoB and 16S rDNA sequence datasets. Both datasets were then grouped in a combined analysis according to the total-evidence method (Huelsenbeck, 1996). The analysis used a branch-and-bound search on all equally weighted characters. Gaps were considered to be missing data. Branch support was estimated using bootstrap analysis (1000 replicates). We added four external taxa: E. coli ATCC 25922T (GenBank accession numbers for rpoB and 16S rDNA: U77436 and AF233451, respectively); Raoultella ornithinolytica ATCC 31898T (AF129447 and AF129441, respectively); Raoultella planticola ATCC 33531T (AF129449 and AF129443, respectively); and Klebsiella pneumoniae ATCC 13883T (U77444 and AF130981, respectively), to test the monophyly of the K. oxytoca strains. The tree was rooted using Rickettsia conorii ATCC VR-141T (rpoB and 16S rDNA GenBank accession numbers are AF076435 and L36105, respectively) as the outgroup.
Arbitrarily amplified DNA polymorphism.
The primer used was the Enterobacterial Repetitive Intergenic Consensus sequence corresponding to ERIC-1R: 5'-ATGTAAGCTCCTGGGGATTCAC-3' (Jones et al., 1999). Amplification was performed with the Ready-To-Go RAPD Analysis Bead kit (Amersham Biosciences) under the conditions recommended by the manufacturer.
GenBank accession numbers.
The sequences determined in this study have been submitted to GenBank and their corresponding accession numbers are presented in Table 1.
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RESULTS |
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). As the majority of K. oxytoca isolates were plasmid-free, and as repeated mating-out experiments failed to transfer blaOXY genes, these genes were assumed to be located on the bacterial chromosome.
blaOXY gene sequences
According to the nucleotide sequences of the blaOXY genes of the 13 clinical isolates in comparison with those of reference strains SL781 and SL911, four isolates possessed a blaOXY-1 gene and nine possessed a blaOXY-2 gene (Tables 2 and 3). All the blaOXY-1 genes of clinical isolates differed from that of the reference strain SL781 by a single nucleotide substitution (G8A) in the promoter region. They also differed from each other and from the reference blaOXY-1 gene within the coding region, either by point mutations leading to amino acid substitutions (Ala237Gly, Ala230Val), silent substitutions (G658A), or by a deletion of the first three or last three nucleotides of the palindromic sequence GCCG, starting at position 71. This resulted in the deletion of the Ala residue at position 12 according to the numbering of Ambler et al. (1991) (Table 2). Similar features were found in the blaOXY-2 genes of clinical isolates with respect to reference strain SL911 (Table 3). Six of the nine blaOXY-2 genes had substitutions in the promoter region, which consisted not only of G8A but also G12T. Five nucleotide substitutions located in the coding region led to amino acid substitutions (Gly20Ser, Asp35Ala, Asp197Asn, Asp255Asn and Val260Ile), whereas two were silent substitutions (A602G and C728A). The deletion of the Ala residue at position 12, which also occurred in the blaOXY-2 gene, resulted from the deletion of the first three or the last three nucleotides of the palindromic sequence GCCG, starting at position 69.
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).
Table 4 shows that the mean percentage of blaOXY gene identity observed within each group of blaOXY genes was >99 %, whereas it was lower (about 87 %) between the two groups of blaOXY genes.
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The sequence of the 16S rDNA fragment studied (387 bp) was identical for the five strains harbouring the blaOXY-1 gene, except for reference strain SL781, in which a single nucleotide substitution was observed. The sequence of the corresponding 16S rDNA fragment in the strains possessing the blaOXY-2 gene was also largely conserved, but four different substitutions were observed, each in a single strain. Comparison of the 16S rDNA consensus sequences of the two types of strains, available as Supplementary Fig. A in IJSEM Online, showed that the two sequences differed from each other by seven nucleotide substitutions, located close to each other in a small fragment from positions 435 to 458 according to the numbering of the E. coli 16S rDNA sequence.
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Table 4 shows that the mean percentage of gene identity for pairs of strains was very high (>99 %) for both the rpoB and 16S rRNA genes within each group of strains, but lower between the two groups of strains: <97 % for the rpoB gene and approximately 97·5 % for the 16S rRNA gene.
Phylogenetic relationships among K. oxytoca and other genera in the Enterobacteriaceae
The phylogenetic trees resulting from the separate analyses of rpoB and 16S rDNA datasets are not shown here. Combination of the datasets globally produced a similar topology, with better robustness and resolution. The combined analysis was computed on 980 molecular characters, of which 61 were parsimony-informative. This led to three trees (length=392 steps, Ciex=0·6250, Hiex=0·3750). The ten unrelated K. oxytoca strains were monophyletic and separated into two clades, corresponding to the strains with the blaOXY-1 gene and the strains with the blaOXY-2 gene. This result was supported by high bootstrap values of 97 and 99 %, respectively. The strict consensus of the three trees is shown in Fig. 1 with the bootstrap values.
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, although the arbitrarily amplified DNA profiles of the ten unlinked strains differed from each other, we can observe two clearly distinct profile types, each related to one of the two types of strains defined by the OXY -lactamase harboured. Thus, two intense bands of approximately 1400 and 1600 bp are always present in strains harbouring the blaOXY-1 gene and never in the strains with the blaOXY-2 gene; likewise, one or two intense bands of approximately 500 bp are always present in strains possessing the blaOXY-2 gene and never in those with the blaOXY-1 gene. |
DISCUSSION |
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-lactamase in relation to up-mutations (Fournier et al., 1995). Effectively, we found the two previously determined types of substitutions located in the -10 region of the promoter of the gene encoding the OXY-1 and OXY-2 -lactamase of the ten clinical isolates (Fournier et al., 1996a). For the three remaining strains, which were phenotypically susceptible to third-generation cephalosporins and aztreonam, no substitution was found in the promoter region.
-Lactamase diversity within the OXY-1 and OXY-2 groups
Among the OXY-1 and OXY-2 -lactamases found in our clinical isolates, some differences were observed in the primary gene sequence of the -lactamase in each group. Regarding the -lactamases of the OXY-1 group, the two amino acid substitutions observed in our strains, Ala237Gly and Ala230Val, have already been described and shown to have no effect on hydrolytic activity (Fournier & Roy, 1997). However, they have never been described alone (Ala237Gly in strain SG12), nor combined with each other without other amino acid substitutions (strains SG49 and SG344), nor combined with the new genetic feature displayed by the OXY-1 -lactamase of strain SG337. Indeed, the blaOXY-1 gene of this strain displayed a deletion of three nucleotides leading to the deletion of the last of the four Ala residues located 12 codons downstream from the starting Met, i.e. located in the signal peptide. By taking into account the published protein sequences of OXY-1 -lactamase and those presented here, eight OXY-1 -lactamases have been molecularly characterized to date (Fournier & Roy, 1997; Wu et al., 1999).
Concerning the OXY-2 -lactamases, those produced by strains SG4 and SG62 corresponded to two of the four published by Fournier et al. (1997). Although they were not epidemiologically related, four of our clinical isolates had an identical OXY-2 -lactamase, characterized by the deletion of an Ala residue belonging to the Ala–Ala–Ala motif located in the signal peptide. By consulting the literature, we found that this deletion is present in two previously published OXY-2 -lactamases, without mention by the authors (Kimura et al., 1996; Wu et al., 1999). Another modification was found in the signal peptide sequence, namely Gly20Ser (strain SG176), which was also published previously, but was associated with other amino acid substitutions (Granier et al., 2002a; Sirot et al., 1998). Finally, strains SG74 and SG81 harboured an OXY-2 -lactamase with a novel amino acid substitution, Val260Ile. As both strains SG74 and SG81 were susceptible to third-generation cephalosporins and aztreonam, substitution Val260Ile does not appear to modify the hydrolytic activity of the enzyme.
Overall, by considering the published OXY-2 -lactamases and those presented here, nine OXY-2 -lactamases have been characterized to date. Comparison of the sequence of published blaOXY genes with those found in our clinical isolates confirmed that the percentage of gene identity was extremely high (>99 %) within each blaOXY gene group, and significantly lower, about 87 %, between the two blaOXY gene groups.
Two clades in the K. oxytoca taxon
By studying three chromosomal genes (blaOXY, 16S rDNA and rpoB) of ten unrelated K. oxytoca strains, we were able to define two clades in the K. oxytoca taxon. This finding is in accordance with the study of Brisse et al. (2001), which had shown, using other genes (namely gyrA and parC) and different typing methods (RAPD and ribotyping), that six clinical isolates of K. oxytoca and reference strain K. oxytoca NCTC 49131 were classified into two clusters. The new relevant point in our study is the demonstration that this genetic delineation was also obtained from the chromosomal -lactamase gene of K. oxytoca, which does not belong to the housekeeping gene family. To our knowledge, it is the first demonstration of a chromosomal -lactamase that is able to divide a taxon into clades. This finding suggests that chromosomal bla genes, which are extremely common in the Enterobacteriaceae, are affected by an evolutionary process, as well as housekeeping genes. Therefore, evolution of the bla gene might also reflect species evolution.
The second significant point of our study is that the 16S rRNA gene, although it has a low evolutionary rate, was also able to define the two clades in the K. oxytoca taxon (Palys et al., 1997). Moreover, another discriminatory gene recently used in parallel with the 16S rRNA gene to establish the phylogenetic relationships of enterobacterial species, namely the rpoB gene, was also able to delineate the two clades (Mollet et al., 1997).
Regarding K. oxytoca strain ATCC 13182T, which was used by Mollet et al. (1997) and Drancourt et al. (2001) to establish the phylogenetic relationships between enterobacterial species, we deduced from the comparison of its 16S rDNA and rpoB sequences (GenBank accession numbers AF129440 and U77442, respectively) with the 16S rDNA and rpoB consensus sequences from this study, that its -lactamase belongs to the OXY-2 -lactamase group. We confirmed this classification by sequencing the blaOXY gene and we found that the OXY-2 -lactamase of this strain differs from the reference sequence (strain SL911) by the substitution Val260Ile (data not shown).
This result means that species identification and determination of the OXY -lactamase category can be achieved by a single PCR, and sequencing of either the 16S rRNA gene or rpoB gene. To state that PCR of the blaOXY gene can also be used to identify the species as well as the category of -lactamase, we have to verify that the primers used are not able to amplify any other bla gene.
Considering the fact that each K. oxytoca isolate is classified into one of the two clades regardless of the gene sequence used (blaOXY, 16S rDNA, rpoB) and that the two clades were delineated with bootstrap values as high as those that delineate the two Raoultella species studied, we suggest that K. oxytoca should be divided into two genetic groups, group oxy-1 represented by K. oxytoca strain SL781 (=CIP 104963) and group oxy-2 by K. oxytoca strain SL911 (=CIP 106098).
The last point resulting from our study is the fact that the two genetic groups of K. oxytoca can be distinguished by using the ERIC-1R PCR method, as the isolates of these two groups display distinct profiles, each with characteristic bands. Such a procedure, if it is confirmed on a larger collection of K. oxytoca isolates, could be carried out in molecular epidemiological studies and in laboratories that do not yet have access to the gene amplification and sequencing methods, which are both time-consuming and expensive (Olive & Bean, 1999).
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ACKNOWLEDGEMENTS |
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E. Walckenaer, L. Poirel, V. Leflon-Guibout, P. Nordmann, and M.-H. Nicolas-Chanoine Genetic and Biochemical Characterization of the Chromosomal Class A {beta}-Lactamases of Raoultella (formerly Klebsiella) planticola and Raoultella ornithinolytica Antimicrob. Agents Chemother., January 1, 2004; 48(1): 305 - 312. [Abstract] [Full Text] [PDF]
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S. A. Granier, V. Leflon-Guibout, F. W. Goldstein, and M.-H. Nicolas-Chanoine New Klebsiella oxytoca {beta}-Lactamase Genes blaOXY-3 and blaOXY-4 and a Third Genetic Group of K. oxytoca Based on blaOXY-3 Antimicrob. Agents Chemother., September 1, 2003; 47(9): 2922 - 2928. [Abstract] [Full Text] [PDF]
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